Ahhgust

STRaitRazor

Pycision

Parses bam files and extracts haplotypes

Haplotypical

Haplotype inference from MPS data

MPSOnWindows

Standard next generation / massively parallel sequencing tools compiled for windows. Includes samtools, bwa and tabix!

RtN

PeptideRMP

SeqLib

C++ htslib/bwa-mem/fermi interface for interrogating sequence data

Ahhgust.github.io

Demixtify

Exome2Proteome

Converts exome sequencing data into predicted proteins in FASTA format. It does so retaining *phase* (CIS variation)

FishAndSnpChips

Estimates genotype likelihoods for Illumina SNP-chip data. Designed for low-template samples

IMGC

GTCtoVCF

Script to convert GTC/BPM files to VCF

ksw2

Global alignment and alignment extension

MacrohapSimulator

math-as-code

a cheat-sheet for mathematical notation in code form

MitoDB

Mitomixture database!

MMDIT

Mitochondrial mixture analysis in R

Neutralome

Source code necessary to model diversity throughout the genome.

ped-sim

Pedigree simulator

PeptideLR

Semicontinuous likelihood ratios for peptides!

RSQLite

R interface for SQLite

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

singularity

SingularityCE is the Community Edition of Singularity, an open source container platform designed to be simple, fast, and secure.